Gene activity, chromosome behavior, and essentially all DNA-based genetic function depend to some extent on the factors that are associated with DNA. Hence, understanding of genetic function and the application of this understanding to medical or other needs calls for the identification of such factors, which can be nucleic acid, protein, lipid, or essentially of any chemical compound. Currently, technologies for the identification of such factors are limited by expense of the approach and, in part a consequence of this, the constraint to focus primarily on highly repeated regions of the genome.